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Added some integration tests for multiple samples 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1861 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-16 15:22:10 +00:00
parent 418e007ca6
commit 07b134a124
1 changed files with 21 additions and 1 deletions
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22
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -34,6 +34,27 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// return true;
//}
// --------------------------------------------------------------------------------------------------------------
//
// testing multi-sample calling
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm EM_POINT_ESTIMATE -lod 5", 1,
Arrays.asList("3c806bb0649a889c242a430f1d5bb7f9"));
executeTest("testMultiSamplePilot1", spec);
}
@Test
public void testMultiSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -lod 5", 1,
Arrays.asList("d41d8cd98f00b204e9800998ecf8427e"));
executeTest("testMultiSamplePilot2", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing calls with SLX, 454, and SOLID data
@ -187,5 +208,4 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("915abf82a04fcd1842f6865501bae67c"));
executeTest("empirical1MbTestBinaryGeli", spec);
}
}